Contacts of the strand formed by residues 1225 - 1234 (chain I) in PDB entry 6ASX
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL1225 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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803I ALA* 5.2 1.3 - - + -
804I PHE 4.2 4.7 - - - +
805I MET* 4.5 15.7 - - + -
1209I GLN* 3.2 4.9 - - - -
1210I ILE* 2.9 34.4 + - - +
1212I LEU* 3.7 41.1 - - + +
1221I PHE* 5.3 7.6 - - + -
1222I GLU 5.0 0.9 - - - +
1223I ARG 3.6 6.7 - - - +
1224I PRO* 1.3 75.0 - - + +
1226I THR* 1.3 68.2 + - - +
1227I VAL 3.7 0.5 + - - -
636J GLY* 3.5 34.1 - - - +
638J SER* 3.7 12.8 - - - -
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Residues in contact with THR1226 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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803I ALA* 3.1 5.9 - - - +
804I PHE* 3.0 46.5 + - + -
1112I ILE* 5.3 1.6 - - + -
1115I THR* 4.0 10.8 - - + -
1116I HIS* 3.9 20.5 + - + +
1208I GLY 4.4 2.0 - - - +
1209I GLN* 3.8 16.9 + - - +
1225I VAL* 1.3 73.8 - - - +
1227I VAL* 1.3 69.2 + - - +
638J SER* 3.0 13.9 + - - -
639J VAL 2.9 24.9 + - - +
640J GLY* 4.1 1.7 - - - -
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Residues in contact with VAL1227 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
801I ARG* 4.1 20.6 - - - +
802I VAL 3.1 8.5 - - - +
803I ALA* 3.7 16.4 - - + -
1088I ASP* 6.4 0.2 - - + -
1094I VAL* 4.6 9.4 - - + -
1115I THR* 3.9 10.2 - - - +
1116I HIS* 4.9 1.2 - - - -
1119I MET* 4.3 12.8 - - + +
1208I GLY 4.0 11.3 + - - +
1210I ILE* 3.7 33.2 - - + -
1212I LEU* 3.7 30.3 - - + -
1225I VAL* 3.7 3.3 + - + +
1226I THR* 1.3 83.0 - - - +
1228I GLY* 1.3 61.2 + - - +
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Residues in contact with GLY1228 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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801I ARG* 3.1 9.9 - - - +
802I VAL* 2.8 28.8 + - - -
1115I THR* 3.6 18.3 - - - +
1119I MET* 3.7 16.4 - - - -
1227I VAL* 1.3 79.6 - - - +
1229I TYR* 1.3 66.9 + - - -
1230I MET 4.1 0.4 - - - -
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Residues in contact with TYR1229 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699I LEU* 4.1 15.1 - - + +
700I VAL* 5.3 1.9 - - - +
799I ASN* 4.5 9.1 - - + +
800I MET* 3.4 8.3 - - - +
801I ARG* 3.4 62.9 + - + +
1114I GLU* 4.0 10.0 - - - +
1115I THR* 3.7 10.2 + - - +
1118I GLY* 3.9 26.0 - - - +
1119I MET* 4.0 12.0 - - + +
1122I LYS* 3.5 53.9 - - + +
1126I ASP* 5.4 1.2 + - - -
1228I GLY* 1.3 76.3 - - - -
1230I MET* 1.3 61.6 + - - +
1231I TYR 4.2 0.5 + - - -
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Residues in contact with MET1230 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
799I ASN* 4.2 1.8 - - - -
800I MET* 2.9 30.5 + - - +
802I VAL* 3.8 19.1 - - + +
804I PHE* 3.7 22.9 - - + -
1068I GLY* 5.2 5.2 - - - -
1069I ARG 6.1 0.7 - - - +
1070I HIS* 6.3 0.2 - - - -
1072I ASN* 4.0 19.7 - - - +
1098I LEU* 4.6 7.6 - - + -
1111I GLN* 3.9 24.5 - - + +
1114I GLU* 4.5 17.0 - - + +
1115I THR* 3.4 23.6 - - - +
1229I TYR* 1.3 74.7 - - - +
1231I TYR* 1.3 65.3 + - - +
1232I MET* 3.4 28.1 + - + +
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Residues in contact with TYR1231 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686I GLN* 5.9 0.2 - - - -
696I ASP 3.9 9.4 - - - -
697I LYS 4.0 0.7 - - - -
698I PRO* 3.7 32.3 - - + -
699I LEU 5.3 2.2 - - - +
700I VAL 5.9 0.7 - - - +
795I ALA* 3.2 5.4 - - - -
796I LEU* 2.6 25.6 + - + -
797I GLY* 2.5 52.6 + - - -
798I GLN* 3.6 15.7 - - - -
799I ASN* 3.7 12.8 - - + +
1068I GLY* 4.3 7.4 - - - -
1069I ARG* 3.8 34.3 + - - +
1114I GLU* 4.0 15.7 + - - +
1229I TYR 4.2 0.6 + - - -
1230I MET* 1.3 76.1 - - - +
1232I MET* 1.3 59.4 + - - +
1233I LEU* 3.8 15.7 - - + +
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Residues in contact with MET1232 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797I GLY* 3.4 1.6 - - - -
798I GLN 2.9 34.8 + - - +
800I MET* 3.7 13.9 - - + +
802I VAL* 5.0 4.9 - - - -
816I ILE* 3.7 31.2 - - + -
828I PHE* 4.3 7.1 - - + -
1066I MET* 4.2 13.2 - - + -
1067I ALA* 3.4 20.9 - - - +
1068I GLY* 4.8 0.9 - - - +
1072I ASN* 5.7 2.5 - - - +
1096I ILE* 3.7 35.0 - - + -
1098I LEU* 4.7 9.6 - - + -
1230I MET* 3.4 26.8 + - + +
1231I TYR* 1.3 76.0 - - - +
1233I LEU* 1.3 62.7 + - - +
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Residues in contact with LEU1233 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685I MET 3.9 21.3 - - - +
686I GLN* 4.0 14.1 - - + -
689I ALA* 3.9 22.2 - - + -
796I LEU* 4.1 9.9 - - + -
797I GLY* 4.2 16.8 - - - +
828I PHE* 4.5 4.9 - - - -
1066I MET* 3.3 6.6 - - - +
1067I ALA* 2.9 33.8 + - + +
1068I GLY 4.2 11.0 - - - +
1069I ARG* 3.9 21.1 - - + -
1231I TYR* 3.8 21.5 - - + +
1232I MET* 1.3 79.8 - - - +
1234I LYS* 1.3 61.1 + - - +
1235I LEU* 4.6 7.6 - - + -
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Residues in contact with LYS1234 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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689I ALA* 3.7 2.3 - - - +
690I VAL* 3.3 43.2 + - + +
692I THR* 5.5 4.6 - - + +
797I GLY* 5.3 1.8 - - - -
828I PHE* 3.4 44.3 + - + +
830I THR* 3.6 15.4 - - + +
1058I ARG 4.0 1.0 + - - -
1059I ARG 2.9 28.5 + - - -
1060I ILE* 4.7 4.4 - - + +
1064I ASP* 4.4 16.8 + - + -
1065I LYS 4.1 6.3 - - - +
1066I MET* 4.3 8.1 - - + -
1233I LEU* 1.3 73.4 - - - +
1235I LEU* 1.3 69.4 + - - +
1238I LEU* 4.0 30.8 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il